We only get this error on random occasions, customer pays for next day special delivery, magento syncs this correctly when order is created, but for some reason when the invoice is created it changes the shipping method to 2nd class or some other, the amounts on the invoice also change so that they do not match up with the money recieved via paypal.
I have also had this type of error with sku variations. Customer order says 2650-Black-M, and magento creates invoice for 2650-Black-XXXL for example!
Now you can imagine the customer complaints I have to deal with as I cannot cross reference every order from ebay with magento sales records.
Hope somebody here can help.